Hapi

Inference of Chromosome-Length Haplotypes Using Genomic Data of
Single Gamete Cells

Inference of chromosome-length haplotypes using a few haploid
gametes of an individual. The gamete genotype data may be generated from various platforms
including genotyping arrays and sequencing even with low-coverage. Hapi simply takes
genotype data of known hetSNPs in single gamete cells as input and report the high-resolution
haplotypes as well as confidence of each phased hetSNPs. The package also includes a module
allowing downstream analyses and visualization of identified crossovers in the gametes.

Introduction

Hapi is a novel easy-to-use and high-efficient algorithm that only requires 3 to 5 gametes to reconstruct accurate and high-resolution haplotypes of an individual. The gamete genotype data may be generated from various platforms including genotyping arrays and sequencing even with low-coverage. Hapi simply takes genotype data of known hetSNPs in single gamete cells as input and report the high-resolution haplotypes as well as the confidence level of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of identified crossovers in the gametes.

Manual and R script

The comprehensive manual of Hapi is available here: Hapi Manual.
R code of the workflow is available here: Hapi Workflow

Installation

Installation from Github

Hapi can be easily installed from Github by running the following command in R:

### Install dependencies ahead

install.packages('devtools')

install.packages('HMM')

devtools::install_github('Jialab-UCR/Hapi')

If the installation fails with the ERROR: object 'enexprs' is not exported by 'namespace:rlang', please install the developmental version of rlang package first.